{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,25]],"date-time":"2025-07-25T09:55:55Z","timestamp":1753437355354,"version":"3.32.0"},"reference-count":21,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2020,3,1]],"date-time":"2020-03-01T00:00:00Z","timestamp":1583020800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2020,3,1]],"date-time":"2020-03-01T00:00:00Z","timestamp":1583020800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11871463","11871462","61671444","61621003"],"award-info":[{"award-number":["11871463","11871462","61671444","61621003"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Quant. Biol."],"published-print":{"date-parts":[[2020,3]]},"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Plateau zokor inhabits in sealed burrows from 2,000 to 4,200\u00a0meters at Qinghai\u2010Tibet Plateau. This extreme living environment makes it a great model to study animal adaptation to hypoxia, low temperature, and high carbon dioxide concentration.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We provide an integrated resource, ZokorDB, for tissue specific regulatory network annotation for zokor. ZokorDB is based on a high\u2010quality draft genome of a plateau zokor at 3,300\u00a0m and its transcriptional profiles in brain, heart, liver, kidney, and lung. The conserved non\u2010coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>ZokorDB provides a general draft gene regulatory network (GRN), <jats:italic>i.e.,<\/jats:italic> potential transcription factor (TF) binds to non\u2010coding regulatory elements and regulates the expression of target genes (TG). Furthermore, we refined the GRN by incorporating matched RNA\u2010seq and DNase\u2010seq data from mouse ENCODE project and reconstructed five tissue\u2010specific regulatory networks.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>A web\u2010based, open\u2010access database is developed for easily searching, visualizing, and downloading the annotation and data. The pipeline of non\u2010coding region annotation for zokor will be useful for other non\u2010model species. ZokorDB is free available at the website (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/bigd.big.ac.cn\/zokordb\/\">bigd.big.ac.cn\/zokordb\/<\/jats:ext-link>).<\/jats:p><\/jats:sec>","DOI":"10.1007\/s40484-020-0195-4","type":"journal-article","created":{"date-parts":[[2020,3,6]],"date-time":"2020-03-06T04:51:26Z","timestamp":1583470286000},"page":"43-50","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["ZokorDB: tissue specific regulatory network annotation for non\u2010coding elements of plateau zokor"],"prefix":"10.1002","volume":"8","author":[{"given":"Jingxue","family":"Xin","sequence":"first","affiliation":[{"name":"<!--1--> CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China"},{"name":"<!--6--> Department of Statistics Department of Biomedical Data Science, Bio\u2010X Program Stanford University Stanford CA 94305 USA"},{"name":"<!--7--> University of Chinese Academy of Sciences Beijing 100049 China"}]},{"given":"Junjun","family":"Hao","sequence":"additional","affiliation":[{"name":"<!--2--> State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China"}]},{"given":"Lang","family":"Chen","sequence":"additional","affiliation":[{"name":"<!--1--> CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China"}]},{"given":"Tao","family":"Zhang","sequence":"additional","affiliation":[{"name":"<!--3--> Key Laboratory of Systems Biology Innovation Center for Cell Signaling Network Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China"}]},{"given":"Lei","family":"Li","sequence":"additional","affiliation":[{"name":"<!--1--> CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China"},{"name":"<!--5--> Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming 650223 China"},{"name":"<!--7--> University of Chinese Academy of Sciences Beijing 100049 China"}]},{"given":"Luonan","family":"Chen","sequence":"additional","affiliation":[{"name":"<!--3--> Key Laboratory of Systems Biology Innovation Center for Cell Signaling Network Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China"},{"name":"<!--5--> Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming 650223 China"}]},{"given":"Wenmin","family":"Zhao","sequence":"additional","affiliation":[{"name":"<!--4--> Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China"}]},{"given":"Xuemei","family":"Lu","sequence":"additional","affiliation":[{"name":"<!--2--> State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China"},{"name":"<!--5--> Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming 650223 China"}]},{"given":"Peng","family":"Shi","sequence":"additional","affiliation":[{"name":"<!--2--> State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China"},{"name":"<!--5--> Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming 650223 China"}]},{"given":"Yong","family":"Wang","sequence":"additional","affiliation":[{"name":"<!--1--> CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China"},{"name":"<!--5--> Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming 650223 China"},{"name":"<!--7--> University of Chinese Academy of Sciences Beijing 100049 China"}]}],"member":"311","published-online":{"date-parts":[[2020,3]]},"reference":[{"key":"e_1_2_7_2_2","first-page":"183","article-title":"A revision of the zokors of subgenus Eospalax.","volume":"2","author":"Fan N.","year":"1982","journal-title":"Acta Theriol. 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